Question: the script colabfold_batch is not generated during installation

[A-Talavera]

What is your question? The script colabfold_batch is not generated during installation

Computational environment

• OS: Ubuntu 22.04

To Reproduce Steps to reproduce the behavior:

1. Follow the instructions for a fresh installation
2. I make sure to export /path/to/localcolabfold/colabfold-conda/bin/ into the PATH (export in the .bashrc)

Expected behavior I get an error message saying: localcolabfold/colabfold-conda/bin/colabfold_batch: not found

Indeed, this file is not listed in that directory. I have tried the installation three times always with the same result

As a workaround I copied that file from the previous version 1.3 into the directory localcolabfold/colabfold-conda/bin and changed the first line "#!/localcolabfold/colabfold-conda/bin/python3.7" to "#!/localcolabfold/colabfold-conda/bin/python3.10" and now the program works.

Do you know why I am getting this weird issue?

One more thing, checking the running script for the previous version I saw that it include these lines to configure the memory usage:

export TF_FORCE_UNIFIED_MEMORY="1" export XLA_PYTHON_CLIENT_MEM_FRACTION="4.0" export XDG_CACHE_HOME="${COLABFOLDDIR}"

Are these lines not needed anymore in the new version?

Thansk a lot in advance. Best regards, Ariel

[hjy-1001]

I have this problem as well. It seems that there is no file named colabfold_batch in /mypath/localcolabfold/colabfold-conda/bin. So even though I added export PATH="/mypath/localcolabfold/colabfold-conda/bin:$PATH" in ~/.bashrc and type source ~/.bashrc, The terminal still outputs: -bash: colabfold_batch: command not found

[alexlevylab]

I also have this exact issue!

• can we get confirmation from the developers that the workaround described above has equivalent functionality to a fully functioning v1.5.0? If yes, I will also implement it

As a workaround I copied that file from the previous version 1.3 into the directory localcolabfold/colabfold-conda/bin and changed the first line "#!/localcolabfold/colabfold-conda/bin/python3.7" to "#!/localcolabfold/colabfold-conda/bin/python3.10" and now the program works.

• I also seem to have some errors regarding memory. The Cache is not big enough in the default folder, so I think it's causing it to skip downloading key parts of the installation. Especially this parameter might matter:

export XDG_CACHE_HOME="${COLABFOLDDIR}"

Thanks, this is a great software and I'm looking forward to the fixed version.

Alex

[TribTrav]

Im having the same issue. However, I cant seem to get the version 1.3 workaround to work. When trying to run colabfold_batch I receive the error:

File "/localcolab/localcolabfold/colabfold-conda/bin/colabfold_batch", line 5, in <module> from colabfold.batch import main ModuleNotFoundError: No module named 'colabfold'

Im not sure if anybody else has run into this issue, or knows how to fix it? I suspect it may be a PATH issue (I dont understand PATH that well yet).

Thank you, Travis

[CNwangbin]

The same error occured: ` install_colabbatch_linux.sh: line 33: cd: /home/wangbin/localcolabfold/colabfold -conda/lib/python3.10/site-packages/colabfold: No such file or directory sed: can't read plot.py: No such file or directory sed: can't read download.py: No such file or directory /share/home/wangbin/localcolabfold/colabfold-conda/bin/python3.10: Error while f inding module specification for 'colabfold.download' (ModuleNotFoundError: No mo dule named 'colabfold')

`

[GriffinYoung]

@CNwangbin this is because you were running this on a machine without git installed.

[RobertArbon]

I had the same issue with git installed.

[emmarl25]

I also have this problem on a Linux cluster, even after exporting the PATH variable and restarting the shell multiple times - would appreciate any clarifications!